Literature DB >> 19443687

Automated high-dimensional flow cytometric data analysis.

Saumyadipta Pyne1, Xinli Hu, Kui Wang, Elizabeth Rossin, Tsung-I Lin, Lisa M Maier, Clare Baecher-Allan, Geoffrey J McLachlan, Pablo Tamayo, David A Hafler, Philip L De Jager, Jill P Mesirov.   

Abstract

Flow cytometric analysis allows rapid single cell interrogation of surface and intracellular determinants by measuring fluorescence intensity of fluorophore-conjugated reagents. The availability of new platforms, allowing detection of increasing numbers of cell surface markers, has challenged the traditional technique of identifying cell populations by manual gating and resulted in a growing need for the development of automated, high-dimensional analytical methods. We present a direct multivariate finite mixture modeling approach, using skew and heavy-tailed distributions, to address the complexities of flow cytometric analysis and to deal with high-dimensional cytometric data without the need for projection or transformation. We demonstrate its ability to detect rare populations, to model robustly in the presence of outliers and skew, and to perform the critical task of matching cell populations across samples that enables downstream analysis. This advance will facilitate the application of flow cytometry to new, complex biological and clinical problems.

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Year:  2009        PMID: 19443687      PMCID: PMC2682540          DOI: 10.1073/pnas.0903028106

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  19 in total

1.  11-color, 13-parameter flow cytometry: identification of human naive T cells by phenotype, function, and T-cell receptor diversity.

Authors:  S C De Rosa; L A Herzenberg; L A Herzenberg; M Roederer
Journal:  Nat Med       Date:  2001-02       Impact factor: 53.440

2.  Beyond six colors: a new era in flow cytometry.

Authors:  Stephen C De Rosa; Jason M Brenchley; Mario Roederer
Journal:  Nat Med       Date:  2003-01       Impact factor: 53.440

Review 3.  Seventeen-colour flow cytometry: unravelling the immune system.

Authors:  Stephen P Perfetto; Pratip K Chattopadhyay; Mario Roederer
Journal:  Nat Rev Immunol       Date:  2004-08       Impact factor: 53.106

4.  Analyzing multivariate flow cytometric data in aquatic sciences.

Authors:  S Demers; J Kim; P Legendre; L Legendre
Journal:  Cytometry       Date:  1992

5.  A new automated flow cytometry data analysis approach for the diagnostic screening of neoplastic B-cell disorders in peripheral blood samples with absolute lymphocytosis.

Authors:  E S Costa; M E Arroyo; C E Pedreira; M A García-Marcos; M D Tabernero; J Almeida; A Orfao
Journal:  Leukemia       Date:  2006-05-25       Impact factor: 11.528

6.  MHC class II expression identifies functionally distinct human regulatory T cells.

Authors:  Clare Baecher-Allan; Elizabeth Wolf; David A Hafler
Journal:  J Immunol       Date:  2006-04-15       Impact factor: 5.422

7.  Immunologic self-tolerance maintained by activated T cells expressing IL-2 receptor alpha-chains (CD25). Breakdown of a single mechanism of self-tolerance causes various autoimmune diseases.

Authors:  S Sakaguchi; N Sakaguchi; M Asano; M Itoh; M Toda
Journal:  J Immunol       Date:  1995-08-01       Impact factor: 5.422

Review 8.  Mapping normal and cancer cell signalling networks: towards single-cell proteomics.

Authors:  Jonathan M Irish; Nikesh Kotecha; Garry P Nolan
Journal:  Nat Rev Cancer       Date:  2006-02       Impact factor: 60.716

9.  Automated in-silico detection of cell populations in flow cytometry readouts and its application to leukemia disease monitoring.

Authors:  Joern Toedling; Peter Rhein; Richard Ratei; Leonid Karawajew; Rainer Spang
Journal:  BMC Bioinformatics       Date:  2006-06-05       Impact factor: 3.169

10.  Genetic analysis of human traits in vitro: drug response and gene expression in lymphoblastoid cell lines.

Authors:  Edwin Choy; Roman Yelensky; Sasha Bonakdar; Robert M Plenge; Richa Saxena; Philip L De Jager; Stanley Y Shaw; Cara S Wolfish; Jacqueline M Slavik; Chris Cotsapas; Manuel Rivas; Emmanouil T Dermitzakis; Ellen Cahir-McFarland; Elliott Kieff; David Hafler; Mark J Daly; David Altshuler
Journal:  PLoS Genet       Date:  2008-11-28       Impact factor: 5.917

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  102 in total

Review 1.  New tools for classification and monitoring of autoimmune diseases.

Authors:  Holden T Maecker; Tamsin M Lindstrom; William H Robinson; Paul J Utz; Matthew Hale; Scott D Boyd; Shai S Shen-Orr; C Garrison Fathman
Journal:  Nat Rev Rheumatol       Date:  2012-05-31       Impact factor: 20.543

2.  Rapid cell population identification in flow cytometry data.

Authors:  Nima Aghaeepour; Radina Nikolic; Holger H Hoos; Ryan R Brinkman
Journal:  Cytometry A       Date:  2011-01       Impact factor: 4.355

3.  Understanding GPU Programming for Statistical Computation: Studies in Massively Parallel Massive Mixtures.

Authors:  Marc A Suchard; Quanli Wang; Cliburn Chan; Jacob Frelinger; Andrew Cron; Mike West
Journal:  J Comput Graph Stat       Date:  2010-06-01       Impact factor: 2.302

4.  flowPeaks: a fast unsupervised clustering for flow cytometry data via K-means and density peak finding.

Authors:  Yongchao Ge; Stuart C Sealfon
Journal:  Bioinformatics       Date:  2012-05-17       Impact factor: 6.937

5.  Application of user-guided automated cytometric data analysis to large-scale immunoprofiling of invariant natural killer T cells.

Authors:  Xinli Hu; Hyun Kim; Patrick J Brennan; Buhm Han; Clare M Baecher-Allan; Philip L De Jager; Michael B Brenner; Soumya Raychaudhuri
Journal:  Proc Natl Acad Sci U S A       Date:  2013-11-04       Impact factor: 11.205

6.  Cellular heterogeneity: do differences make a difference?

Authors:  Steven J Altschuler; Lani F Wu
Journal:  Cell       Date:  2010-05-14       Impact factor: 41.582

Review 7.  A Cancer Biologist's Primer on Machine Learning Applications in High-Dimensional Cytometry.

Authors:  Timothy J Keyes; Pablo Domizi; Yu-Chen Lo; Garry P Nolan; Kara L Davis
Journal:  Cytometry A       Date:  2020-06-30       Impact factor: 4.355

8.  Discriminative variable subsets in Bayesian classification with mixture models, with application in flow cytometry studies.

Authors:  Lin Lin; Cliburn Chan; Mike West
Journal:  Biostatistics       Date:  2015-06-03       Impact factor: 5.899

9.  A framework for analytical characterization of monoclonal antibodies based on reactivity profiles in different tissues.

Authors:  Elizabeth Rossin; Tsung-I Lin; Hsiu J Ho; Steven J Mentzer; Saumyadipta Pyne
Journal:  Bioinformatics       Date:  2011-08-16       Impact factor: 6.937

Review 10.  Bioinformatic approaches to augment study of epithelial-to-mesenchymal transition in lung cancer.

Authors:  Tim N Beck; Adaeze J Chikwem; Nehal R Solanki; Erica A Golemis
Journal:  Physiol Genomics       Date:  2014-08-05       Impact factor: 3.107

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